having pkg-resources in the pip freeze output doesn't seem very useful and might even be harmful. (I suspect it's why running pip-sync from pip-tools uninstalls pkg-resources from the virtual environment, subtly breaking the environment thereby.) Is there any good reason why pip freeze lists pkg-resources instead of omitting it, too? As far as I remember, it didn't list it on Ubuntu 14.04 (with Python 3.4).

I don't know why exactly this happens. This happened to me with a different package that was actually essential for my project. The solution I found was to edit the requirements.txt with the latest available version on PyPi. One possibility, I'm guessing, is the version that was initially installed is no longer available on PyPi.
– owobeidOct 1 '16 at 14:07

It's amazing that there isn't an answer for this yet...
– AdamOct 18 '16 at 12:45

This caused a production push to fail for me, so I am very curious as to the answer / resolution.
– Craig WrightOct 19 '16 at 19:39

Sorry, I don't quite remember what the issue was back then, and I don't have an Ubuntu system handy at the moment. IIRC, pkg-resources is an integral part of the virtualenv and needed by Python, pip or maybe virtualenv itself. Not sure what exactly would stop working when it's missing.
– das-gJan 9 at 8:50